id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7336 AlphaFold reporting old files anthony.morgan@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.5-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Run Colabfold. Folder called ""Prediction #2"" appears in the Downloads folder. Problem: if I *move* the folder out of Downloads, the next prediction (for a different protein sequence — same session?) displays the correct structure inside CX, but the NEW 'Prediction 2' folder that appears contains the previous OLD protein files (not the ones associated new one). Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold Populating font family aliases took 282 ms. Replace uses of missing font family ""Calibri"" with one that exists to avoid this cost. > alphafold predict > MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET Running AlphaFold prediction AlphaFold prediction finished Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2 Chain information for best_model.pdb #1 --- Chain | Description A | No description available > show surfaces > close > alphafold predict > MAAPPGEYFSVGSAVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET Running AlphaFold prediction > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/TPC2-GG_iTASSER/model1.pdb"" format pdb No such file/path: /Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/TPC2-GG_iTASSER/model1.pdb AlphaFold prediction finished Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2 Chain information for best_model.pdb #1 --- Chain | Description A | No description available > close > alphafold predict > MAAPPGEYFSVGSQVSCRTCQEQRLQGAVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTET Running AlphaFold prediction AlphaFold prediction finished Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2 Chain information for best_model.pdb #1 --- Chain | Description A | No description available > alphafold predict > MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTET Running AlphaFold prediction AlphaFold prediction finished Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2 Chain information for best_model.pdb #2 --- Chain | Description A | No description available > close > alphafold predict > MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPNHADILLINLQYVSEVEIINDRTETPPVGTVSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGRPYEGVQTMRIKVIEGGPLPFAFDILATSFMYGSRTFIKYPADIPDFFKQSFPEGFTWERVTRYEDGGVVTVTQDTSLEDGELVYNVKVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTDIALKVDGGGHLHCNFVTTYRSKKTVGNIKMPGVHAVDHRLERIEESDNETYVVQREVAVAKYSNLGGGMDELYK > minimize false Running AlphaFold prediction > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT/af69_relaxed_rank_1_model_1.pdb"" Chain information for af69_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available > color bfactor 1072 atoms, 69 residues, atom bfactor range 40 to 95.6 > color bfactor #1 palette alphafold 1072 atoms, 69 residues, atom bfactor range 40 to 95.6 > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm > FL-domain/af69_relaxed_rank_1_model_1.pdb"" Chain information for af69_relaxed_rank_1_model_1.pdb #2 --- Chain | Description A | No description available > Matchmaker #2 to #1 Unknown command: Matchmaker #2 to #1 > Matchmaker #1 to #2 Unknown command: Matchmaker #1 to #2 > hide #2 models > show #2 models > hide #2 models > show #2 models > select #2/A:9 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 175 atoms, 178 bonds, 13 residues, 1 model selected > select up 1067 atoms, 1075 bonds, 69 residues, 1 model selected > select up 2139 atoms, 2155 bonds, 138 residues, 2 models selected > select up 2139 atoms, 2155 bonds, 138 residues, 2 models selected > select down 1067 atoms, 1075 bonds, 69 residues, 1 model selected > select up 2139 atoms, 2155 bonds, 138 residues, 2 models selected > lighting soft > lighting simple > close > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT/af69_relaxed_rank_1_model_1.pdb"" format pdb Chain information for af69_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available > close > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm > FL-domain/af69_relaxed_rank_1_model_1.pdb"" format pdb Chain information for af69_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available Alignment identifier is 1/A > select /A:14-18,24-33,38-42,49-53,59-64 505 atoms, 501 bonds, 31 residues, 1 model selected > close > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera X_Dropbx/LSm12/LION/LSm > FL-domain/af69_relaxed_rank_1_model_1.pdb"" Chain information for af69_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available Alignment identifier is 1/A > select /A:14-18,24-33,38-42,49-53,59-64 505 atoms, 501 bonds, 31 residues, 1 model selected > select /A:69 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:69 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:14-18,24-33,38-42,49-53,59-64 505 atoms, 501 bonds, 31 residues, 1 model selected > close AlphaFold prediction finished Results in /Users/anthonymorgan/Downloads/ChimeraX/AlphaFold/prediction_2 Chain information for best_model.pdb #1 --- Chain | Description A | No description available Alignment identifier is 1/A > select > /A:14-18,24-33,38-42,49-53,59-64,86-96,99-110,115-124,165-173,178-188,191-201,220-227,230-240,246-257,270-281,287-297 1209 atoms, 1211 bonds, 149 residues, 1 model selected > select /A:54-56,132-134,136-138,144-146,158-160,283-285,300-302 172 atoms, 168 bonds, 21 residues, 1 model selected > select /A:62 8 atoms, 7 bonds, 1 residue, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 49 atoms, 48 bonds, 6 residues, 1 model selected > select up 2428 atoms, 2480 bonds, 310 residues, 1 model selected > select down 49 atoms, 48 bonds, 6 residues, 1 model selected > alphafold pae #1 file ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT-mRuby3/af69_predicted_aligned_error_v1.json"" Number of residues in structure ""best_model.pdb #1"" is 310 which does not match PAE matrix size 69. This can happen if the AlphaFold model has been trimmed to match an experimental structure, or if residues have been deleted. The full-length AlphaFold model must be used to show predicted aligned error. > alphafold pae #1 file ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT- > mRuby3/af69_unrelaxed_rank_1_model_1_scores.json"" Number of residues in structure ""best_model.pdb #1"" is 310 which does not match PAE matrix size 69. This can happen if the AlphaFold model has been trimmed to match an experimental structure, or if residues have been deleted. The full-length AlphaFold model must be used to show predicted aligned error. > alphafold pae #1 file ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT- > mRuby3/af69_unrelaxed_rank_1_model_1_scores.json"" Number of residues in structure ""best_model.pdb #1"" is 310 which does not match PAE matrix size 69. This can happen if the AlphaFold model has been trimmed to match an experimental structure, or if residues have been deleted. The full-length AlphaFold model must be used to show predicted aligned error. > close > open ""/Users/anthonymorgan/Dropbox/Work temp/Chimera > X_Dropbx/LSm12/LION/LION-WT-mRuby3/af69_relaxed_rank_1_model_1.pdb"" Chain information for af69_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available OpenGL version: 4.1 INTEL-14.6.18 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir9,1 Processor Name: Dual-Core Intel Core i3 Processor Speed: 1.1 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 512 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0) Software: System Software Overview: System Version: macOS 10.15.5 (19F101) Kernel Version: Darwin 19.5.0 Time since boot: 8 days 6:54 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a5c Revision ID: 0x0007 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Structure Prediction fixed all ChimeraX